Website:WormMine

Background

Based on the Getting Started Tutorial:

   http://intermine.org/wiki/GettingStarted

Getting the source

You'll need both the intermine source code as well as various wormbase "website-intermine" repositories.

> cd /usr/local/wormbase    // or whatever
> mkdir intermine ; cd intermine
> svn co svn://subversion.flymine.org/branches/intermine_0_98
> ln -s intermine_0_98 intermine

Fetch the WormBase-specific elements of intermine, currently maintained as separate repositories.

// The master directory, containing model and code for fetching/parsing datasets
> cd intermine
> git clone http://github.com/WormBase/website-intermine-master wormbase-mine
// sources
> cd bio/sources
> git clone git://github.com/WormBase/website-intermine-sources.git wormbase-mine

Users and Groups

sudo adduser intermine  // will be the user connecting to the mine database
sudo passwd intermine xxxxxx

Install Prerequisites (Debian)

(see http://intermine.org/wiki/Prerequisites)

 $ sudo apt-get install sun-java6-sdk
 $ sudo apt-get install ant

Postgres

 $ sudo apt-get install postgresql

Set up postgres users and create a database:

TH: THIS IS A HACK. I don't fully grok postgres' authentication config.

[tharris@wb-dev: bin]> sudo -u postgres psql -d template1 -U postgres
psql (8.4.8)
Type "help" for help.

template1=# CREATE USER intermine WITH PASSWORD 'xxxxxxx';
CREATE ROLE
template1=# create database wormmine;
template1=# create database items-wormmine;
CREATE DATABASE
template1=# GRANT ALL PRIVILEGES ON DATABASE wormmine to intermine;
template1=# GRANT ALL PRIVILEGES ON DATABASE items-wormmine to intermine;
template1=#  \q

Tomcat

Via the package manner:

 $ sudo apt-get install tomcat6

 // Or via a stable binary
 $ curl -O http://mirror.csclub.uwaterloo.ca/apache/tomcat/tomcat-6/v6.0.33/bin/apache-tomcat-6.0.33.tar.gz
 $ tar -zxfv apache-tomcat-6* ; cd apache-tomcat*
 // startup.sh and shutdown.sh are found in apache-tomcat*/bin/

// Set up users. If installed via the package manager
$ sudo emacs /etc/tomcat6/tomcat-users.xml

<tomcat-users>
 <role rolename="manager"/>
 <user username="manager" password="manager" roles="manager"/>
</tomcat-users>

Edit the port in /etc/tomcat6/server.xml that Tomcat is listening on to something amenable with their architecture (for example 9999).

Data Sources

Data sources are collected at /usr/local/wormbase/intermine/data, and within that directory by version.

/usr/local/wormbase/intermine/data/WSVERSION/SOURCE/DATA_TYPE

eg:

/usr/local/wormbase/intermine/data/WS227/wormbase/gff3/
/usr/local/wormbase/intermine/data/WS227/dbsnp
/usr/local/wormbase/intermine/data/WS227/uniprot

WormBase specific modifications

The following directories currently contain WormMine-specific modifications that are NOT under version control:

• The entire intermine/wormmine directory. Relocating it and symlinking intermine/wormine -> our/source/repo doesn't work.

• The intermine/bio/sources directory. This *can* be relocated in wormmine/project.xml, but build paths in sources need to be updated, too.